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- PDB-4uxx: Structure of delta4-DgkA with AMPPCP in 9.9 MAG -

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Basic information

Entry
Database: PDB / ID: 4uxx
TitleStructure of delta4-DgkA with AMPPCP in 9.9 MAG
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / ATP ANALOGUE / DGKA / DIACYLGLYEROL KINASE / IN MESO CRYSTALLIZATION / LIPID CUBIC PHASE / LIPIDIC CUBIC PHASE / LIPID MESOPHASE / LIPIDIC MESOPHASE / MEMBRANE PROTEIN / 9.9 MAG / MONOACYLGLYCEROL / NON- HYDROLYZABLE ATP ANALOGUE / NUCLEOTIDE ANALOGUE
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / phosphorylation / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Helix Hairpins - #3610 / DAGK family / Diacylglycerol kinase, prokaryotic / Diacylglycerol kinase (DAGK) superfamily / Prokaryotic diacylglycerol kinase / Prokaryotic diacylglycerol kinase signature. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ACETATE ION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsLi, D. / Vogeley, L. / Caffrey, M.
CitationJournal: Nat.Commun. / Year: 2015
Title: Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase.
Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / ...Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / Weierstall, U. / Zatsepin, N.A. / Cherezov, V. / Liu, W. / Bandaru, S. / English, N.J. / Gati, C. / Barty, A. / Yefanov, O. / Chapman, H.N. / Diederichs, K. / Messerschmidt, M. / Boutet, S. / Williams, G.J. / Marvin Seibert, M. / Caffrey, M.
History
DepositionAug 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 2.0Mar 6, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _atom_site.occupancy / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.1Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIACYLGLYCEROL KINASE
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,89720
Polymers42,7223
Non-polymers3,17517
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-83.7 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.940, 72.940, 195.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-1126-

NA

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein DIACYLGLYCEROL KINASE / DAGK / DIGLYCERIDE KINASE / DGK


Mass: 14240.527 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PTRCHISB-DGKA-DELTA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

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Non-polymers , 8 types, 30 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE PROTEIN CONTAINS AN N-TERMINAL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN ...THE PROTEIN CONTAINS AN N-TERMINAL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN HAS FOUR MUTATIONS. THEY ARE I53V, I70L, M96L AND V107D.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.85 %
Description: FOUR CRYSTALS WERE USED FOR THE NATIVE DATA SET. A SINGLE CRYSTAL WAS USED FOR THE ZN-ANOMALOUS DATA SET.
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5.6
Details: 7-10 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 4 ...Details: 7-10 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 4 DEGREES CELCIUS WITH THE 9.9 MONOACYLGLYCEROL (MONOOLEIN, 9.9 MAG) AS THE HOSTING LIPID.CRYSTALS WERE SOAKED WITH 5-10 MM AMPPCP, 60 MM ZINC ACETATE BEFORE HARVESTING.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03320, 1.28238
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21.282381
ReflectionResolution: 2.7→53.07 Å / Num. obs: 17218 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 68.67 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.9
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.6 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZE5

3ze5


Resolution: 2.701→53.075 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 29.62 / Stereochemistry target values: ML
Details: THERE ARE THREE NCS-RELATED MOLECULES IN THE ASYMMETRIC UNIT BUT NCS GLOBAL RESTRAINTS WERE NOT USED IN THE REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2577 850 4.9 %
Rwork0.2191 --
obs0.2212 17165 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.91 Å2
Refinement stepCycle: LAST / Resolution: 2.701→53.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 207 13 2796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122843
X-RAY DIFFRACTIONf_angle_d0.7493810
X-RAY DIFFRACTIONf_dihedral_angle_d13.0271044
X-RAY DIFFRACTIONf_chiral_restr0.036454
X-RAY DIFFRACTIONf_plane_restr0.003460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7009-2.87010.34031270.2782620X-RAY DIFFRACTION97
2.8701-3.09170.30271260.25242682X-RAY DIFFRACTION100
3.0917-3.40270.25521510.24162667X-RAY DIFFRACTION100
3.4027-3.8950.25691550.21412712X-RAY DIFFRACTION100
3.895-4.90670.20211550.18622755X-RAY DIFFRACTION100
4.9067-53.08520.28651360.22562879X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0517-0.5384-3.02525.08421.44673.90870.31080.13250.3732-0.26040.2931-0.11110.0270.5119-0.58630.65970.1736-0.09370.6592-0.12080.554659.0327-15.339624.6987
24.571-0.784-2.14054.3061.73351.8698-0.12870.71020.1641-0.31180.1710.0672-1.265-0.16930.10490.79510.1557-0.00430.5098-0.00530.459348.5967-16.75116.3047
33.0171-1.1638-0.86843.32430.30238.2956-0.0243-0.0081-0.00320.0345-0.27670.1411-0.2178-0.21890.37950.71370.25920.00350.4931-0.04370.591541.3466-14.326629.479
44.80161.9331-3.59063.2199-0.33135.3797-0.4171.46910.5888-0.8560.1671-0.09951.0242-0.81780.1091.10990.0607-0.07890.9255-0.0410.281539.8532-38.971513.0505
52.4553-0.72621.50083.4661-1.27091.1231-0.2339-0.0404-0.04530.170.0174-0.06660.80490.0340.33960.91930.32420.06730.5659-0.0190.455351.7071-33.051724.1616
65.156-0.5581-0.42393.41551.99755.990.0663-0.131-0.00240.45310.1744-0.23630.24390.6955-0.1690.44230.22020.01280.4246-0.05250.535857.0297-24.514322.2502
74.1454.9559-4.0486.9092-5.87165.0481-0.32540.7815-0.3064-0.91271.20070.4934-1.0937-1.5862-1.21451.12880.30440.06011.1618-0.09090.821531.8101-15.244814.6023
82.9057-0.02322.37543.4274-1.39384.6922-0.2885-0.7511-0.0880.78180.98840.2534-0.5368-1.5314-0.44011.14680.45380.18051.18570.0810.837230.136-24.261931.7308
92.3988-0.1049-0.96332.04971.67542.00050.11460.2820.05770.1452-0.07310.3141-0.3687-1.78-0.05350.59480.25530.00410.62280.01580.500239.5808-23.423821.006
104.6521-0.2365-1.71164.75241.27988.9088-0.25610.334-0.10780.55210.06360.38450.573-1.35420.23640.69720.04080.06680.5265-0.07120.673640.5818-33.100520.6706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 7 THROUGH 51 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 52 THROUGH 91 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 92 THROUGH 120 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 6 THROUGH 27 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 28 THROUGH 83 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 84 THROUGH 121 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 16 THROUGH 28 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 29 THROUGH 51 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 52 THROUGH 82 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 83 THROUGH 120 )

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